Software Open Access

IceBreaker

Olek, Mateusz; Cowtan, Kevin; Webb, Donovan; Chaban, Yuriy; Zhang, Peijun

Other(s)
Hatton, Daniel; Gerstel, Markus; Horstmann, Anna

The Icebreaker software for ice gradient estimation and removal on cryoEM micrographs.

External job for calling IceBreaker grouping within Relion 3.1 in_parts is input star file from relion picking job in_mics is previous grouping job directory

Run in main Relion project directory

PROCESSING THE MICROGRAPHS

To process the micrographs use the ib_job script

As an input, it takes a .star file with a list of micrographs to process, e.g. micrographs_ctf.star

In the 'Params' tab, you have to add a label mode which can take values group (it will group areas with similar ice thickness) or flatten (it will improve contrasts locally trying to remove the ice gradient).

In the Running tab use the slider to select the number of threads.

The output from this job is a new set of micrographs.

PROCESSING THE PARTICLES

As 'Input micrographs' it takes micrographs 'grouped' with the previous script. As 'Input particles' any star file with particles from jobs like Extract particles, 2D classes, etc. It takes no additional parameters and this is single-threaded. As a result, additional parameter column (_rlnHelicalTubeID) with estimated ice thickness value for each particle will be added.

 

Files (36.3 kB)
Name Size
icebreaker_em-0.3.4-py3-none-any.whl
md5:164a15d98ee811fea2dfbbb569fa9e59
22.7 kB Download
icebreaker_em-0.3.4.tar.gz
md5:0489d2902330b3a56cef3449d456e4d5
13.6 kB Download
93
10
views
downloads
All versions This version
Views 9393
Downloads 1010
Data volume 181.5 kB181.5 kB
Unique views 7979
Unique downloads 66

Share

Cite as